Changes between Version 5 and Version 6 of net.sf.basedb.reggie/notes423
- Timestamp:
- Sep 4, 2019, 2:35:02 PM (5 years ago)
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net.sf.basedb.reggie/notes423
v5 v6 29 29 - `<align-hisat>/<mark-duplicates-options>` 30 30 31 == 3. Update BASE to BASE 3.15.2 == 31 32 32 == 3. Install Reggie 4.23 and run the installation wizard == 33 This version is needed because it includes the **Tag batch item importer** that is needed in a later stop to import barcodes for the MIPs libraries. 33 34 35 == 4. Install Reggie 4.23 and run the installation wizard == 34 36 35 == 4. Set a value for the Pipeline annotation on existing items ==37 == 5. Set a value for the Pipeline annotation on existing items == 36 38 37 39 Almost all existing items from **Library** and downstream must be given a value for the **Pipeline** annotation. The table below specifies the value … … 49 51 || Software || Demuxing, Merging || - || RNAseq || 50 52 51 == 5. Other updates to existing items ==53 == 6. Other updates to existing items == 52 54 53 55 Existing **Hardware** items of type=**Sequencer** should be updated with a value for the **!FlowCellType** annotation. It should be either !NextSeq or !HiSeq. 54 56 55 == 6. New items that should be created ==57 == 7. New items that should be created == 56 58 57 59 || **Item type** || **Subtypes** || **Additional settings** || **Comment** || 58 || Protocol || DNANormalization || !TargetAmount, !TargetMinimalAmount, !TargetVolume, MIPS_Pool || The protocol to use for normalizing DNA that should go into the MIPs pipeline. ||60 || Protocol || DNANormalization || !TargetAmount, !TargetMinimalAmount, !TargetVolume, MIPS_Pool || The protocol to use for normalizing DNA that should go into the MIPs pipeline. If no protocol exists, the option to pre-normalize DNA items (in the DNA/RNA/FlowThrough registration wizard) will not be enabled by default. Thus, it is recommended that a `DNANormalization` protocol is created only when needed. || 59 61 || Protocol || Library preparation || !LibPrepTarget=MIPs || One or more protocols that will appear in the "MIPs library registration" wizard || 60 62 || Protocol || Pooling || !LibPrepTarget=MIPs || One or more protocols that will appear in the MIPs pooling wizard || … … 64 66 || Software || Merging || Pipeline=MIPs || One or more software entries that will appear in the MIPs demux wizard (merge section) || 65 67 66 == 7. Barcodes and barcode template plates == 68 69 == 8. Barcodes and barcode template plates == 67 70 68 71 Most of the barcode information (such as the sequences, positions, etc.) should be available as a file that can be used with batch importers. Some steps need to be done manually. … … 90 93 91 94 92 == 8. User accounts for MIPs pipeline ==95 == 9. User accounts for MIPs pipeline == 93 96 94 97 A user account that should work with the MIPs pipeline need to have the following group/role memberships:
